I will try to make this brief. I know Soul Eater ended ages ago and I just started watching it. I'm at season 3. I'm just curious about how they become weapons? I know that one is born as a weapon, but what happens physically? I might be overthinking it, but I am just curious.

1 Answer
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The so called weapons are a artificial race, created due to inhumane human/witch experimentation. We do not know how the actual physical transformation happens. Nor how the experimentation ultimatetly led to this race

These experiments known to create these weapons was originally discovered by Eibon and Death, whilst trying to find a way to create peace between the humans and the witches. Due to the inhumane practices required to create such demon weapons they decided to lock the exact steps away.

But as you learn later on in the story as well. Arachnid, with her spiders, managed to obtain this information, and started her own experimentation. Ultimatly leading to the race currently known as Demon Weapons

The ´weapons´ Race, as a social construct, is a group of people who share similar and distinct physical characteristics

This particular race came to be 800 years before the start of the series, during the time Eibon and Death sought a way to create peace between humans and witches.

Inspired by the Great Old one (Excalibur) they decided to start human experimentation to create something similar. They managed to find out that by killing a witch and extracting a soul they could create a demon weapon.

Due to the inhumanity they sealed away the instructions for doing so. Yet Arachne using her spiders managed to oversee this, and started her own experimentation. Leading her to combining a weapon, and a witches soul. This concluded in a new 'race' now known as the 'demon weapons' or weapons for short. Or as we known them, the humans transforming into weapons. - SE Wiki

Excalibur is a Great old one? well it certainly explains why he keeps calling us "Fools!"
– Memor-XOct 13 '15 at 22:15

Important to note that, by taking the spin off "Soul Eater NOT" in account, the experiment unlocked the weapon potential in humanity, be it by genes or magic. So people that have the ability to become weapons seem to awaken during their childhood and adolescence.
– Sigfried666Oct 13 '15 at 22:28